rs12456880

chr18-846743-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.29 in 151,946 control chromosomes in the GnomAD database, including 7,200 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.29 (7200 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.290 AC: 43965 AN: 151830 Hom.: 7186 Cov.: 32

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.248

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.290 AC: 44023 AN: 151946 Hom.: 7200 Cov.: 32 AF XY: 0.292 AC XY: 21720 AN XY: 74274

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.539

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.248

Alfa AF: 0.228 Hom.: 4718

Bravo AF: 0.304

Asia WGS AF: 0.384 AC: 1335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.3
Dann	Benign	0.52

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12456880; hg19: chr18-846744;